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The BioGRID interaction database: 2019 update
2018
Nucleic Acids Research
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The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the curation and archival storage of protein, genetic and chemical interactions ...
BioGRID now captures chemical interaction data, including chemical-protein interactions for human drug targets drawn from the DrugBank database and manually curated bioactive compounds reported in the ...
ACKNOWLEDGEMENTS The authors thank John Aitchison, Brenda Andrews, Gary Bader, Anastasia Baryshnikova ...
doi:10.1093/nar/gky1079
pmid:30476227
pmcid:PMC6324058
fatcat:72ppbdg3vbbhzfeugxmqu7athm
The BioGRID interaction database: 2013 update
2012
Nucleic Acids Research
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This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. ...
The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions ...
ACKNOWLEDGEMENTS The authors thank Chris Grove, Paul Sternberg and Anastasia Baryshnikova for ongoing collaborative development of the Genetic Interaction Structured Terminology. ...
doi:10.1093/nar/gks1158
pmid:23203989
pmcid:PMC3531226
fatcat:nmn2ijk3qje6jfpsgpzgk2p2nm
The Comparative Toxicogenomics Database: update 2017
2016
Nucleic Acids Research
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The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between chemicals and gene products, and their relationships to diseases. ...
Core CTD content (chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature) are integrated with each other as well as with select external datasets to generate ...
(A) CTD's new 'Exposure Studies' query page (http://
D976 Nucleic Acids Research, 2017, Vol. 45, Database issue
Figure 3 3 Figure 3. ...
doi:10.1093/nar/gkw838
pmid:27651457
pmcid:PMC5210612
fatcat:povogyqyofcebnljc3jnl4fnoq
MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes
2017
Database: The Journal of Biological Databases and Curation
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MiRIAD is a database with an interactive and user-friendly online interface that has been facilitating research on intragenic miRNAs. In this article, we present a major update. ...
Although the previous version solely reported protein interactions, the update features a separate network analysis view that can either be accessed V C The Author(s) through the submission of a list of ...
Acknowledgements The authors thank Gustavo S. Franc¸a for working on the previous miRIAD version as well as Anamaria A. Camargo and Luiz F. L. Reis for their valuable suggestions. ...
doi:10.1093/database/bax053
pmid:29220447
pmcid:PMC5569676
fatcat:j6h6gfuwgbezfa2r2mlyjsucca
KiPho: malaria parasite kinome and phosphatome portal
2017
Database: The Journal of Biological Databases and Curation
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Additionally, we have incorporated relevant and manually curated data, which will be updated from time to time with the availability of new information. ...
The Plasmodium kinases and phosphatases play an essential role in the regulation of substrate reversible-phosphorylation and overall cellular homeostasis. ...
Database, Vol. 2017, Article ID bax063 ...
doi:10.1093/database/bax063
pmid:29220464
pmcid:PMC5737071
fatcat:svl76ahoivd5vescvimp6nzkme
Measuring pathway database coverage of the phosphoproteome
2021
PeerJ
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We first determined the global coverage of each database at both the protein and phosphosite level. ...
Finally, we looked in detail at the coverage of each database over six experimental datasets. ...
ACKNOWLEDGEMENTS The authors thank Daniel Esposito, Samuel Lee and Dharmesh Bhuva for technical support.
ADDITIONAL INFORMATION AND DECLARATIONS ...
doi:10.7717/peerj.11298
pmid:34113485
pmcid:PMC8162239
fatcat:yx4zibz3cvcm7h344ie3g2ge5u
Protein-Protein Interaction Interface Database Development based on Protein Network
2017
IJARCCE
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Protein-Protein interaction interface database (PPIIDB) is developing on the basis of cellular and biological processes of protein-protein interaction interfaces of protein network. ...
energy (∆G), Cluster Coefficient (CC), Connectivity, Degree of node or Degree of network, Euclidean Distance between interacted proteins, Network Interaction Modularity (Im), size of interface or Voronoi ...
ANALYSES OF VARIOUS DATABASES We have analysis various Databases, like the PINT, Protorp, HPRD, BioGRID, BIND, IntAct, MIPS, APID, DIP, and MINT these all databases provide the lists of experimental and ...
doi:10.17148/ijarcce.2017.63211
fatcat:lotwvtx6jna4zofxz4drm7ohfi
PICKLE 3.0: Enriching the human Meta-database with the mouse protein interactome extended via mouse-human orthology
2020
Bioinformatics
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Summary The PICKLE 3.0 upgrade refers to the enrichment of this human protein-protein interaction (PPI) meta-database with the mouse protein interactome. ...
The relational scheme of PICKLE 3.0 has been amended to exploit the Mouse Genome Informatics (MGI) mouse-human ortholog gene pair collection, enabling (i) the extension through orthology of the mouse interactome ...
Introduction Protein InteraCtion KnowLegdE (PICKLE) meta-database has been developed to consistently integrate primary human PPI datasets (Gioutlakis et al, 2017; Klapa et al, 2013) . ...
doi:10.1093/bioinformatics/btaa1070
pmid:33367505
pmcid:PMC8034533
fatcat:q4tmssyesnaujcabqpvtcpclqq
YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules
2017
Database: The Journal of Biological Databases and Curation
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in the GM. ...
Since Cbf1-Met4-Met32 is known to regulate genes in sulfur amino acid biosynthesis pathway, we test the overlap between the set of genes in the sulfur amino acid biosynthesis pathway and the set of genes ...
In the future, we plan to improve YGMD as follows. First, we will keep updating our database once updated data in SGD, YEASTRACT, BioGRID, CoopTFD and YeastNet are available. ...
doi:10.1093/database/bax085
pmid:29220473
pmcid:PMC5691354
fatcat:qhrubmmjy5fijb7o7af76u6pdq
How helpful are the protein-protein interaction databases and which ones?
[article]
2019
bioRxiv
pre-print
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Protein-protein interactions (PPIs) are critical, and so are the databases and tools (resources) concerning PPIs. ...
Overall, hPRINT, STRING and IID together retrieved ~94% of 'total' protein interactions available in the databases. The coverage of certain databases was skewed for some gene-types. ...
Acknowledgements The authors thank colleagues at BdataA and Shodhaka Life Sciences Pvt. Ltd. for assistance in gathering some of the PPI data and analysis. ...
doi:10.1101/566372
fatcat:f46uga34djaarbpao2wgvzldu4
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology
2017
PLoS ONE
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used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. ...
PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. ...
.0186039 October 12, 2017 17 / 17 ...
doi:10.1371/journal.pone.0186039
pmid:29023571
pmcid:PMC5638325
fatcat:nvhuozyp2je33gw7m23epeler4
Predicted rat interactome database and gene set linkage analysis
2020
Database: The Journal of Biological Databases and Curation
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To facilitate molecular pharmacology studies in rats, we present the predicted rat interactome database (PRID), which is a database of high-quality predicted functional gene interactions with balanced ...
PRID integrates functional gene association data from 10 public databases and infers 305 939 putative functional associations, which are expected to include 13.02% of all rat protein interactions, and ...
Some of these databases integrate the experimentally reported protein-protein interactions, such as RGD (14) , BioGrid (15) and IntAct (16) . ...
doi:10.1093/database/baaa086
pmid:33216897
pmcid:PMC7678787
fatcat:g4fsyhzbt5g7xniqgvvdz2r2ai
mPPI: a database extension to visualize structural interactome in a one-to-many manner
2021
Database: The Journal of Biological Databases and Curation
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Protein–protein interaction (PPI) databases with structural information are useful to investigate biological functions at both systematic and atomic levels. ...
From the perspective of the display and function of PPI, as well as the structural binding interface, the related database and resources are summarized. ...
The duplication was because most indexed entries were from literature mining, which has not excluded the submission of database updates. ...
doi:10.1093/database/baab036
pmid:34156447
fatcat:jehgi5sty5birgsr6dez3iwr4u
mutTCPdb: a comprehensive database for genomic variants of a tropical country neglected disease—tropical calcific pancreatitis
2018
Database: The Journal of Biological Databases and Curation
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Several existing databases such as the dbSNP, Uniprot, miRTarBase2.0, HGNC, PFAM, KEGG, PROSITE, MINT, BIOGRID 3.4 and Ensemble Genome Browser 87 were queried to collect information specific to the gene ...
The database is highly curated for diseasespecific gene variants and provides complete information on function, transcript information, pathways, interactions, miRNAs and PubMed references along with remarks ...
Acknowledgement A.S. is thankful to Shiv Nadar University for providing all the necessary support to perform this study. Conflict of interest. None declared. ...
doi:10.1093/database/bay043
pmid:30053238
pmcid:PMC6059086
fatcat:sactgq45obefxkbiaysbl7ib6u
The Comparative Toxicogenomics Database: update 2019
2018
Nucleic Acids Research
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The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases ...
These updates continue to improve CTD and help inform new testable hypotheses about the etiology and mechanisms underlying environmentally influenced diseases. ...
Here, we provide our biennial database update and describe our newly released chemical-phenotype module, advanced query and display tools for exposure science data, an extensive update to the MEDIC disease ...
doi:10.1093/nar/gky868
pmid:30247620
pmcid:PMC6323936
fatcat:4qvewpc42jhsvic7phptfwy6im
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